Lamune tells the story of a boy named Kenji and his childhood friend Nanami. Although, everyone seems to know that they have a relationship, neither are determined to push it anymore than close friends. The story goes through flashbacks, explaining why they are such close friends and any action doesn't seem to push them apart, but draw them closer.

One day, a very tall transfer student shows up and Risa immediately falls for him, as she has had bad luck with boys in the past because she is tall. There is a girl that Otani likes as well, so Risa and Otani decide to put aside their differences and help each other get their love interests. But as they get to know each other better, Risa's feelings for Otani begin to blossom.

On his first day at his new school, 12-year old Ritsuka Aoyagi meets a mysterious 20-year old man named Soubi Agatsuma. He claims to be a good friend of Ritsuka's brother, Seimei, who was recently murdered, and the suspicious organization called 'Septimal Moon' may be responsible for the death. As Ritsuka quickly finds out, Seimei and Soubi acted as a pair involved in spell battles. Now Soubi is Ritsuka's fighter, and Ritsuka is his 'sacrifice'. Together, they challenge the organization to find out the truth behind Seimei's death and the reason for Ritsuka's amnesia.